[Insight-users] Centering slices extracted from a volume

[Bill Lorensen]

The problem is creating 2D direction cosines from the 3D direction cosines.

I think Hans Johnson recently checked in a temporary fix for this:

http://public.kitware.com/cgi-bin/viewcvs.cgi/Code/BasicFilters/itkExtractImageFilter.txx?root=Insight&view=log

Bill

On Tue, Nov 11, 2008 at 7:34 PM, Richard Beare <richard.beare at gmail.com> wrote:
> Hi,
>
> I'm running into issues preparing histology and MR images for registration.
>
> I'm extracting slices from the MRI using the ExtractImageFilter and
> attempting to reset the origin using ChangeInformationImageFilter
>
> If I start with a 2D image (such as the histology scans) then the
> centering works correctly, as judged using fslview - i.e cursors in
> the middle reports a coordinate of (0,0).
>
> However, when starting with the 3D data, nothing seems to work unless
> I pretend that the output image is 3D with only one slice. There seems
> to be an interaction between the extraction and the orientation
> information that produces incorrect results. - for example the
> DIrection information appears to become invalid:
>
>  Spacing: [0.0299728, 0.03]
>  Origin: [5.61499, 10.3093]
>  Direction:
> -1 0
> 0 0
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